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1 <?xml version="1.0"?>
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2
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3 <tool id="concordance_report_1" name="Compute intra-NGS concordance">
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4 <description>over targeted regions in a genome</description>
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5 <version_string>kappa_report -v</version_string>
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6 <command interpreter="perl">kappa_report -q $target_bed $coding_gtf $input_ngs_calls1 $input_bam1 $coverage_cutoff1 $input_ngs_calls2 $input_bam2 $coverage_cutoff2 $out_summary_table</command>
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7 <inputs>
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8 <param format="gtf" name="coding_gtf" type="data" label="Coding regions" help="This must be the same (GTF) file used to define the coding regions for the HGVS annotation of the NGS variant calls"/>
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9 <param format="bed" name="target_bed" type="data" label="Target sequencing regions" help="e.g. a BED file from the Shared Data 'Exome target regions' folder, corresponding to the capture kit used for sequencing the sample"/>
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10 <param format="achri_snp_table" name="input_ngs_calls1" type="data" label="HGVS annotated NGS variant calls for genotyping method #1"/>
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11 <param format="bam" name="input_bam1" type="data" label="Mapped reads file (BAM) that was used to generate the NGS variant calls for genotyping method #1"/>
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12 <param type="integer" name="coverage_cutoff1" value="20" min="1" max="40" label="Report method #1 calls only for positions with read depth equal to or greater than..."/>
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13 <param format="achri_snp_table" name="input_ngs_calls2" type="data" label="HGVS annotated NGS variant calls for genotyping method #2"/>
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14 <param format="bam" name="input_bam2" type="data" label="Mapped reads file (BAM) that was used to generate the NGS variant calls for genotyping method #2"/>
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15 <param type="integer" name="coverage_cutoff2" value="20" min="1" max="40" label="Report method #2 calls only for positions with read depth equal to or greater than..."/>
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16 </inputs>
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17 <outputs>
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18 <data name="out_summary_table" format="tabular" label="Concordance summary (shared, unique calls, etc.)"/>
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19 </outputs>
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20
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21 <tests>
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22 </tests>
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23
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24 <help>
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25 **What it does**
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26
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27 This tool reports several statistics comparing the genotypes derived from two next-gen sequencing runs. This is intended to measure methodological consistency,
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28 assuming the samples for both methods are from the same individual. When coverage is good (typically 10x for colorspace, 20x for base space), there should be a large
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29 (>= 95%) overlap between the calls if they are reasonably accurate.
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30 </help>
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31
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32 </tool>
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